qdsfit/QDS.py
2013-06-14 08:44:34 +02:00

668 lines
25 KiB
Python
Executable File

#!/usr/bin/env python
# -*- encoding: utf-8 -*-
import os,sys
import re
import signal
from PyQt4.QtCore import *
from PyQt4.QtGui import *
from PyQt4.uic import *
from matplotlib.backends.backend_qt4agg import FigureCanvasQTAgg as FigureCanvas
from matplotlib.backends.backend_qt4agg import NavigationToolbar2QTAgg as NavigationToolbar
import matplotlib.pyplot as plt
import matplotlib.colors
import numpy as N
import scipy.odr as O
import scipy.optimize as opt
import MatplotlibWidget
import QDSMain
import PeakWidget
import ConductivityWidget
from data import Data
#import yaff
def sigint_handler(*args):
"""Handler for the SIGINT signal."""
sys.stderr.write('\r')
if QMessageBox.question(None, '', "Are you sure you want to quit?",
QMessageBox.Yes | QMessageBox.No,
QMessageBox.No) == QMessageBox.Yes:
QApplication.quit()
def id_to_color(id):
colors = ['b', 'r','g','c','m','y','k']
conv = matplotlib.colors.ColorConverter()
return conv.to_rgb(colors[id%len(colors)])
def tau_peak(f,a,b):
tau = (N.sin( N.pi*a/2./(b+1) )/N.sin( N.pi*a*b/2./(b+1) ))**(1/a)
tau /= 2*N.pi*f
return tau
def hn(p,nu):
delta_eps,tau,a,b = p
om = 2*N.pi*nu
Phi = N.arctan( (om*tau)**a*N.sin(N.pi*a/2.)/(1.+(om*tau)**a*N.cos(N.pi*a/2.)) )
e_loss = delta_eps * (1+ 2*(om*tau)**a * N.cos(N.pi*a/2.) + (om*tau)**(2.*a) )**(-b/2.)*N.sin(b*Phi)
e_stor = delta_eps * (1+ 2*(om*tau)**a * N.cos(N.pi*a/2.) + (om*tau)**(2.*a) )**(-b/2.)*N.cos(b*Phi)
return 2*e_loss
def multi_hn(p,nu):
conductivity = p[1]
cond_beta = p[2]
om = 2*N.pi*nu
e_loss = conductivity/om**cond_beta
e_loss += p[0]
#for key, igroup in groupby(p[3:], lambda x: x//4):
for i in xrange(len(p[3:])/4):
delta_eps, tau, a, b = p[3+i*4:3+(i+1)*4]
#delta_eps, tau, a, b = list(igroup)
#print delta_eps,tau,a,b
#a = 0.5 *(1 + N.tanh(a))
#b = 0.5 *(1 + N.tanh(b))
Phi = N.arctan( (om*tau)**a*N.sin(N.pi*a/2.)/(1.+(om*tau)**a*N.cos(N.pi*a/2.)) )
e_loss += 2*delta_eps * (1+ 2*(om*tau)**a * N.cos(N.pi*a/2.) + (om*tau)**(2.*a) )**(-b/2.)*N.sin(b*Phi)
#e_stor = delta_eps * (1+ 2*(om*tau)**a * N.cos(N.pi*a/2.) + (om*tau)**(2.*a) )**(-b/2.)*N.cos(b*Phi)
return e_loss
def mini_func(p,x, y):
res = y - multi_hn(p,x)
# apply weights
res /= 1/y
return N.sqrt(N.dot(res,res))
def conductivity(p, nu):
c = p[0]/(2*N.pi*nu)**p[1]
return c
def hnfit(delta_eps, tau, points):
x = [point[0] for point in points]
y = [point[1] for point in points]
dat = O.Data(x,y)
mod = O.Model(hn)
odr = O.ODR(dat,mod, [delta_eps, tau, 1, 1], ifixb=(0,0,1,1), ifixx=(0,), maxit=1000)
odr.run()
odr.output.pprint()
return odr.output.beta
def fit_odr(x,y,p0, fixed):
dat = O.Data(x,y, 1.0/y)
mod = O.Model(multi_hn)
odr = O.ODR(dat, mod, p0, ifixx=(0,), ifixb=fixed, maxit=2000)
odr.run()
return odr.output.beta
def fit_lbfgsb(x,y,p0, fixed):
# TODO fixed parameters…
bounds = [(0,None), (0,1)]
for i in xrange(len(p0[3:])/4):
bounds.append((1e-4,1e12)) # delta_eps
bounds.append((1e-12,1e3)) # tau
bounds.append((0.1,1)) # a
bounds.append((0.1,1)) # b
x,f_minvalue, info_dict = opt.fmin_l_bfgs_b(mini_func, p0,
fprime=None,
args=(x,y),
approx_grad=True,
bounds=bounds,
iprint=0,
maxfun=4000)
if info_dict['warnflag'] != 0:
print info_dict["task"]
return x
def fit_anneal(x,y,p0,fixed):
bounds = [(0,1e14), (0,1)]
for i in xrange(len(p0[2:])/4):
bounds.append((1e-4,1e12)) # delta_eps
bounds.append((1e-12,1e3)) # tau
bounds.append((0.1,1)) # a
bounds.append((0.1,1)) # b
ret = opt.anneal(mini_func, p0,
args=(x,y),
maxeval=20000,
maxiter=30000,
lower=[b[0] for b in bounds],
upper=[b[1] for b in bounds],
dwell=100,
full_output=1)
#pmin, func_min, final_Temp, cooling_iters,accepted_tests, retval
#retval : int
#Flag indicating stopping condition::
# 0 : Points no longer changing
# 1 : Cooled to final temperature
# 2 : Maximum function evaluations
# 3 : Maximum cooling iterations reached
# 4 : Maximum accepted query locations reached
# 5 : Final point not the minimum amongst encountered points
print "Stop reason", ret
return ret[0]
class Conductivity(QObject):
changedData = pyqtSignal()
def __init__(self, mpl=None):
QObject.__init__(self)
super(Conductivity, self)
self.widget = ConductivityWidget.ConductivityWidget()
self.widget.changedTable.connect(self.updateData)
self.mpl_line = None
self.mpl_line_static = None
self.mpl = mpl
def getParameter(self):
p = self.widget.getTable()
return p
def getFixed(self):
p = self.widget.fixedParameter()
return p
def setParameter(self, eps_static=None, sigma=None, sigma_N=None):
self.widget.updateTable(eps_static, sigma, sigma_N)
self.updateData()
def updateData(self):
# get current axis limits
x_min, x_max = self.mpl.canvas.axes.get_xlim()
y_min, y_max = self.mpl.canvas.axes.get_ylim()
nu = N.logspace(N.log10(x_min), N.log10(x_max), 1024)
eps_static, sigma, sigma_N = self.getParameter()
y = conductivity([sigma, sigma_N],nu)
y_static = N.ones(len(nu))*eps_static
# clip data to axes limits
mask_static = (y_static < y_max) & (y_static > y_min)
# clip data to axes limits
mask = (y < y_max) & (y > y_min)
#mask = mask_static = N.ones(1024, dtype='bool')
if self.mpl_line == None:
self.mpl_line, = self.mpl.canvas.axes.loglog(nu[mask],y[mask],'k--',label="Cond.", animated=True) # peak
else:
self.mpl_line.set_xdata(nu[mask])
self.mpl_line.set_ydata(y[mask])
if self.mpl_line_static == None:
self.mpl_line_static, = self.mpl.canvas.axes.loglog(nu[mask_static],
y_static[mask_static],
'k:',
label=r"$\epsilon_S$",
animated=True) # peak
else:
self.mpl_line_static.set_xdata(nu[mask_static])
self.mpl_line_static.set_ydata(y_static[mask_static])
self.changedData.emit()
class Peak(QObject):
changedData = pyqtSignal()
def __init__(self, id=None, mpl=None):
QObject.__init__(self)
super(Peak, self).__init__()
self.color = id_to_color(id)
self.widget = PeakWidget.PeakWidget()
self.widget.setId(id)
self.widget.setColor(map(int, [255*i for i in self.color]))
self.widget.changedTable.connect(self.updatePeak)
self.mpl = mpl
self.mpl_line = None
def getParameter(self):
p = self.widget.peakParameter()
return p
def getFixed(self):
p = self.widget.fixedParameter()
return p
def setParameter(self, delta_eps=None, tau=None, a=None, b=None):
self.widget.updateTable(delta_eps, tau, a, b)
self.updatePeak()
def updatePeak(self):
# get current axis limits
x_min, x_max = self.mpl.canvas.axes.get_xlim()
y_min, y_max = self.mpl.canvas.axes.get_ylim()
nu = N.logspace(N.log10(x_min), N.log10(x_max), 2048)
y = hn(self.getParameter(),nu)
# clip data to axes limits
mask = (y < y_max) & (y > y_min)
y = y[mask]
nu = nu[mask]
if self.mpl_line == None:
self.mpl_line, = self.mpl.canvas.axes.loglog(nu,y,'--',label="Peak %i"%(self.widget.id), animated=True) # peak
self.mpl_line.set_color(self.color)
else:
self.mpl_line.set_xdata(nu)
self.mpl_line.set_ydata(y)
self.changedData.emit()
class AppWindow(QMainWindow):
def __init__(self, parent=None):
super(AppWindow, self).__init__(parent)
self.ui = QDSMain.Ui_MainWindow()
self.ui.setupUi(self)
self.picked_artist = None
self.data = None
self.Conductivity = None
self._lines = dict()
self.peakId = 0
self.peakBoxes = {}
## menubar
fileMenu = self.menuBar().addMenu("File")
openFile = QAction("&Open",self)
openFile.setShortcut(QKeySequence.Open)
openFile.triggered.connect(self.openFile)
fileMenu.addAction(openFile)
# fitting methods
fitMenu = self.menuBar().addMenu("Fit")
# lm
fit_lmAction = QAction("&Levenberg-Marquardt",self)
fitMenu.addAction(fit_lmAction)
# lbfgsb
fit_lbfgsbAction = QAction("&L-BFGS-B",self)
fitMenu.addAction(fit_lbfgsbAction)
# Simulated Annealing
fit_annealAction = QAction("&Simulated Annealing",self)
fitMenu.addAction(fit_annealAction)
self.signalMapper = QSignalMapper(self)
for i, fit_action in enumerate([fit_lmAction, fit_lbfgsbAction, fit_annealAction
]):
self.signalMapper.setMapping(fit_action,i)
fit_action.triggered.connect(self.signalMapper.map)
self.signalMapper.mapped.connect(self.fitData)
# save fitted values
self.ui.actionSave_FitResult.triggered.connect(self.saveFit)
# he plot area, a matplotlib widget
self.mplWidget = PlotWidget(self.ui.mplWidget)
self.mplWidget.canvas.draw()
self.mplWidget.updateGeometry()
# what to do with CIDs?
self.cid = []
self.cid.append( self.mplWidget.canvas.mpl_connect("button_press_event", self.onclick) )
self.cid.append( self.mplWidget.canvas.mpl_connect("pick_event", self.pick) )
self.cid.append( self.mplWidget.canvas.mpl_connect("button_release_event", self.mpl_button_release) )
self.mplWidget.toolbar.spanSelectedTrigger.connect(self.set_fit_xlimits)
def resizeEvent(self,evt):
self.mplWidget.canvas.draw()
self.mplWidget._bg_cache = self.mplWidget.canvas.copy_from_bbox(self.mplWidget.canvas.axes.bbox)
for line in self.mplWidget.canvas.axes.get_lines():
line.set_animated(False)
self.mplWidget.canvas.draw()
for line in self.mplWidget.canvas.axes.get_lines():
line.set_animated(True)
def saveFit(self):
if not os.path.exists("fitresults.log"):
f = open("fitresults.log","w")
# write header
f.write('# T ')
if self.Conductivity != None:
f.write("e_s sig pow_sig ")
for i,pb in enumerate(self.peakBoxes):
f.write("e_inf_%i tau_%i alpha_%i beta_%i"%(i,i,i,i))
f.write('\n')
f.flush()
else:
f = open("fitresults.log","a")
#f.write("%3.2f "%(self.data.meta["T"]))
pars = list(self.fitresult)
pars.insert(0,self.data.meta["T"] )
print pars
N.savetxt(f,N.array([pars,]),fmt="%.5g", delimiter=" ")
f.close()
def set_fit_xlimits(self,xmin,xmax):
self.data.fit_limits = (xmin, xmax, None,None)
def mpl_button_release(self,event):
if self.picked_artist:
if not event.inaxes: # moved outside the plot, add back to original position
self.mplWidget.canvas.axes.add_artist(self.picked_artist)
else: # we move one of the three points determinig the peak
self.picked_artist.set_xdata(event.xdata)
self.picked_artist.set_ydata(event.ydata)
self.mplWidget.canvas.axes.add_artist(self.picked_artist)
for peak in self.peakBoxes.keys():
peak.updatePeak()
self.picked_artist = None
self.mplWidget.canvas.draw_idle()
def pick(self,event):
self.picked_artist = event.artist
event.artist.remove()
self.mplWidget.canvas.draw_idle()
def addCond(self, pos):
if self.Conductivity != None:
return
self.statusBar().showMessage("Click on graph")
self.Conductivity = Conductivity(mpl=self.mplWidget)
self.Conductivity.changedData.connect(self.updatePlot)
self.Conductivity.setParameter(0, 1/(pos[0]/pos[1]/2/N.pi), 1.0)
self.ui.scrollAreaWidgetContents.layout().addWidget(self.Conductivity.widget)
self.Conductivity.widget.ui.removeButton.clicked.connect(self.delCond)
def delCond(self):
self.cond_param = None
self.cond = None
self.Conductivity.mpl_line.remove()
self.Conductivity.mpl_line_static.remove()
del self.Conductivity
self.Conductivity = None
self.updatePlot()
def addPeak(self, pos):
self.peakId += 1
self.statusBar().showMessage("Select Peak Position")
peak = Peak(id=self.peakId, mpl=self.mplWidget)
# connect to delPeak
peak.widget.ui.removeButton.clicked.connect(self.delPeak)
peak.setParameter(delta_eps=pos[1], tau=1/(2.*N.pi*pos[0]), a=1, b=1)
peak.changedData.connect(self.updatePlot)
self.peakBoxes[peak]=None
for pb in self.peakBoxes.keys():
self.ui.scrollAreaWidgetContents.layout().addWidget(pb.widget)
self.updatePlot()
def delPeak(self):
deletePeaks = []
for i in xrange(self.ui.scrollAreaWidgetContents.layout().count()):
print i
for i,peak in enumerate(self.peakBoxes.keys()):
if peak.widget.isHidden():
peak.mpl_line.remove()
deletePeaks.append(peak)
for peak in deletePeaks:
self.peakBoxes.pop(peak)
self.updatePlot()
def fitData(self, method):
if self.Conductivity != None:
start_parameter = list(self.Conductivity.getParameter())
fixed_params = [ i for i in self.Conductivity.getFixed() ]
else:
start_parameter = [0,0,1]
fixed_params = [0,0,0]
for pb in self.peakBoxes.keys():
[ start_parameter.append(i) for i in pb.getParameter() ]
[ fixed_params.append(i) for i in pb.getFixed() ]
fit_methods = [fit_odr, fit_lbfgsb, fit_anneal]
print "StartParameter",start_parameter
print "FixedParameter",fixed_params
print "Limits (xmin, xmax, ymin, ymax)", self.data.fit_limits
_freq, _fit = self.data.get_data()
result = fit_methods[method](_freq, _fit.imag, start_parameter, fixed_params)
self.fitresult = result
for i,pb in enumerate(self.peakBoxes.keys()):
delta_eps, tau, a, b = result[3+i*4:3+(i+1)*4]
pb.setParameter(delta_eps, tau, a, b )
e_static,sigma, sigma_N = result[:3]
if self.Conductivity != None:
self.Conductivity.setParameter(e_static,sigma,sigma_N)
print "*** FIT RESULTS ***"
print u"\u03c3"
print u"\u0394\u03b5"
self.updatePlot()
def onclick(self, event):
"""
Handles the clicks on the matplotlib figure canvas
"""
if self.ui.actionAdd_Peak.isChecked():
x,y = event.xdata,event.ydata
self.addPeak((x,y))
self.ui.actionAdd_Peak.setChecked(False)
self.statusBar().clear()
if self.ui.actionAdd_Cond.isChecked():
x,y = event.xdata,event.ydata
self.addCond((x,y))
self.ui.actionAdd_Cond.setChecked(False)
self.statusBar().clear()
def openFile(self):
path = unicode(QFileDialog.getOpenFileName(self, "Open file"))
# TODO anaylize file (LF,MF, HF) and act accordingly
data = N.loadtxt(path, skiprows=4)
numpat = re.compile('\d+\.\d+')
try:
for line in open(path).readlines():
if re.search("Fixed", line) or re.search("Temp", line):
Temp = float(re.search(numpat, line).group())
print "Temperature found in file:",Temp
break
else:
print "No Temperature found in file"
#Temp = QInputDialog.getDouble(self, "No temperature found in data set","Temperature/K:", value=Temp)[0]
except:
Temp = QInputDialog.getDouble(self, "No temperature found in data set","Temperature/K:", value=0.0)[0]
# mask the data to values > 0 (loglog plot)
mask = (data[:,1]>0) & (data[:,2]>0) #& (data[:,2]>1e-3) & (data[:,0] > 1e-2)
_freq = data[mask,0]
_die_stor = data[mask,1]
_die_loss = data[mask,2]
# clear the figure
self.mplWidget.canvas.axes.clear()
#if self.data != None:
# self.data.remove_curves()
self.data = Data(_freq, _die_stor, _die_loss)
self.data.meta["T"]=Temp
self.data.data_curve, = self.mplWidget.canvas.axes.loglog(self.data.frequency,
self.data.epsilon.imag,
'b.',
markersize=4,
label="Data",
animated=True)
self.mplWidget.canvas.axes.set_xlim(_freq.min(), _freq.max())
self.mplWidget.canvas.axes.set_xlabel("frequency/Hz", fontsize=16)
self.mplWidget.canvas.axes.set_ylabel(u'\u03B5"', fontsize=16)
self.mplWidget.canvas.axes.autoscale(True)
self.legend = self.mplWidget.canvas.axes.legend(title="T=%.2f"%Temp)
for line in self.mplWidget.canvas.axes.get_lines():
line.set_animated(False)
self.mplWidget.canvas.axes.grid()
self.mplWidget.canvas.draw()
for line in self.mplWidget.canvas.axes.get_lines():
line.set_animated(True)
self.legend.set_animated(True)
self.mplWidget.canvas.axes.autoscale(False)
self.mplWidget._bg_cache = self.mplWidget.canvas.copy_from_bbox(self.mplWidget.canvas.axes.bbox)
self.updatePlot()
def updatePlot(self):
nu = self.data.frequency
fit = N.zeros(len(nu))
for peak in self.peakBoxes.keys():
params = peak.getParameter()
fit += hn(params,nu)
if self.Conductivity != None:
print "Cond. given"
params = self.Conductivity.getParameter()[1:]
fit += conductivity(params, nu)
fit += self.Conductivity.getParameter()[0] # eps static
# clip data to axes limits
y_min, y_max = self.mplWidget.canvas.axes.get_ylim()
mask = (fit < y_max) & (fit > y_min)
#mask = N.ones(len(fit), dtype="bool")
if self.data.fitted_curve == None:
self.data.fitted_curve, = self.mplWidget.canvas.axes.loglog(nu[mask],fit[mask],
'k-',
alpha=0.5,
label="Sum",
animated=True)
else:
self.data.fitted_curve.set_xdata(nu[mask])
self.data.fitted_curve.set_ydata(fit[mask])
# update lines
self.mplWidget.canvas.restore_region(self.mplWidget._bg_cache)
self.legend = self.mplWidget.canvas.axes.legend(title = "T=%.2f"%(self.data.meta["T"]) )
self.legend.set_animated(True)
for animated_artist in self.mplWidget.canvas.axes.findobj(match=lambda x: x.get_animated()):
#print "updatePlot: animated artist:",animated_artist
self.mplWidget.canvas.axes.draw_artist(animated_artist)
self.mplWidget.canvas.blit( self.mplWidget.canvas.axes.bbox )
class PlotWidget(QWidget):
def __init__(self, parent=None):
QWidget.__init__(self)
super(PlotWidget, self).__init__(parent)
self.mplwidget = MatplotlibWidget.MatplotlibWidget(hold=True,
xlim=(1e-2,1e7),
xscale='log',
yscale='log')
self.canvas = self.mplwidget.figure.canvas # shortcut
self.canvas.axes.grid(True)
self.bbox_size = self.canvas.axes.bbox.size
print "PlotWidget",self.bbox_size
#self.toolbar = NavigationToolbar(self.mplwidget, parent)
self.toolbar = CustomToolbar(self.canvas, self.mplwidget, parent)
layout = QVBoxLayout(parent)
layout.addWidget(self.canvas)
layout.addWidget(self.mplwidget)
layout.addWidget(self.toolbar)
self._bg_cache = None
class CustomToolbar(NavigationToolbar):
# our spanChanged signal
spanSelectedTrigger = pyqtSignal(float, float, name='spanChanged')
def __init__(self, plotCanvas, plotWidget, parent=None):
NavigationToolbar.__init__(self, plotCanvas, plotWidget, coordinates=True)
self.canvas = plotCanvas
# Span select Button
#self.span_button = QAction(QIcon("border-1d-right-icon.png" ), "Span", self)
self.span_button = QAction( QIcon(QPixmap(":/icons/fit_limits.png")), "Span", self)
self.span_button.setCheckable(True)
self.cids = []
self.cids.append(self.canvas.mpl_connect('button_press_event', self.press))
self.cids.append(self.canvas.mpl_connect('motion_notify_event', self.onmove))
self.cids.append(self.canvas.mpl_connect('button_release_event', self.release))
self.cids.append(self.canvas.mpl_connect('draw_event', self.update_background))
# act.setCheckable(True)
# add actions before the coordinates widget
self.insertAction(self.actions()[-1], self.span_button)
self.buttons={}
self._pressed = False
self.background = None
self.span = None
self.istart = 0
self.iend = 0
self.xstart = 0
self.xend = 0
def set_span(self,x1,x2):
#trans = blended_transform_factory(self.axes.transData, self.axes.transAxes)
cur = self.span.get_xy()
cur[0,0] = x1
cur[1,0] = x1
cur[2,0] = x2
cur[3,0] = x2
self.span.set_xy(cur)
def ignore(self, event):
# 'return ``True`` if *event* should be ignored'
return event.inaxes!=self.canvas.axes or event.button !=1
def update_background(self, event):
#if self.canvas.axes is None:
# raise SyntaxError,"Need an axes reference!"
self.background = self.canvas.copy_from_bbox(self.canvas.axes.bbox)
def press(self, event):
if self.span_button.isChecked():
if self.background is None:
self.update_background()
else:
self.canvas.restore_region(self.background)
self.xstart = event.xdata
self.istart = event.x
if self.span is None:
self.span = self.canvas.axes.axvspan(event.xdata, event.xdata, alpha = 0.10, color = "k", animated=False)
else:
self.set_span(event.xdata, event.xdata)
self._pressed = True
def onmove(self,event):
if self.span_button.isChecked() and self._pressed and not self.ignore(event):
self.set_span(self.xstart, event.xdata)
self.update()
def update(self):
self.canvas.restore_region(self.background)
self.canvas.axes.draw_artist(self.span)
for line in self.canvas.axes.get_lines():
self.canvas.axes.draw_artist(line)
self.canvas.blit(self.canvas.axes.bbox)
def release(self,event):
self.span_button.setChecked(False)
self.xend = event.xdata
self.iend = event.x
if self.iend < self.istart:
self.iend,self.istart = self.istart,self.iend
print "released",self.xstart,self.xend
if self._pressed:
if self.ignore(event):
self.istart = 0
self.spanSelectedTrigger.emit(self.xstart,self.xend)
self._pressed = False
if __name__ == '__main__':
signal.signal(signal.SIGINT, sigint_handler)
app = QApplication(sys.argv)
timer = QTimer()
timer.start(1000) # Check every second for Strg-c on Cmd line
timer.timeout.connect(lambda: None)
main = AppWindow()
main.showMaximized()
main.raise_()
sys.exit(app.exec_())